Genomic Abundance Is Not Predictive Of Tandem Repeat Localization In Grass Genomes

ASU Author/Contributor (non-ASU co-authors, if there are any, appear on document)
Matt Estep, Assistant Professor (Creator)
Appalachian State University (ASU )
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Abstract: Highly repetitive regions have historically posed a challenge when investigating sequence variation and content. High-throughput sequencing has enabled researchers to use whole-genome shotgun sequencing to estimate the abundance of repetitive sequence, and these methodologies have been recently applied to centromeres. Previous research has investigated variation in centromere repeats across eukaryotes, positing that the highest abundance tandem repeat in a genome is often the centromeric repeat. To test this assumption, we used shotgun sequencing and a bio-informatic pipeline to identify common tandem repeats across a number of grass species. We find that de novo assembly and subsequent abundance ranking of repeats can successfully identify tandem repeats with homology to known tandem repeats. Fluorescent in-situ hybridization shows that de novo assembly and ranking of repeats from non-model taxa identifies chromosome domains rich in tandem repeats both near peri-centromeres and elsewhere in the genome.

Additional Information

Paul Bilinski, Yonghua Han, Matthew B. Hufford, Anne Lorant, Pingdong Zhang, Matt C. Estep, Jiming Jiang, & Jeffrey Ross-Ibarra. (2016). "Genomic Abundance Is Not Predictive Of Tandem Repeat Localization In Grass Genomes." PLoS ONE (open access) 12(6): e0177896. Version Of Record Available At www.PloS
Language: English
Date: 2016
grass genomes, genomic abundance, localization, molecular biology

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